DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=1.248e^-1)
Null hypothesis is not rejected (p>0.05).
Interpretation: NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test

Covariate	p-value	Significance
In_3R_K	0.04315

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

768 significant hits at p-value < 0.001.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	5383614	2L_5383614_SNP [dm3] 2L_5383614_SNP [dm6]	T	G	4.728e^-6	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2L	3010795	2L_3010795_SNP [dm3] 2L_3010795_SNP [dm6]	G	T	4.896e^-6	1	INTRON CG17265
2R	15794780	2R_15794780_SNP [dm3] 2R_19907275_SNP [dm6]	C	T	9.029e^-6	1	INTERGENIC
3L	12457397	3L_12457397_SNP [dm3] 3L_12464297_SNP [dm6]	G	C	1.101e^-5	1	INTRON eyg	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8525032	3L_8525032_SNP [dm3] 3L_8531932_SNP [dm6]	A	C	1.364e^-5	1	SYNONYMOUS_CODING foi	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	15290875	X_15290875_SNP [dm3] X_15396842_SNP [dm6]	G	A	1.546e^-5	1	SYNONYMOUS_CODING Cngl
X	17210040	X_17210040_SNP [dm3] X_17316007_SNP [dm6]	T	C	1.891e^-5	1	INTRON B-H2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad
2L	12762886	2L_12762886_SNP [dm3] 2L_12762886_SNP [dm6]	T	C	2.429e^-5	1	INTERGENIC
2L	2123343	2L_2123343_SNP [dm3] 2L_2123343_SNP [dm6]	A	C	2.770e^-5	1	INTERGENIC
X	12517277	X_12517277_DEL [dm3] X_12623244_DEL [dm6]	CC	C	3.510e^-5	1	DOWNSTREAM CR44568 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
X	5878203	X_5878203_SNP [dm3] X_5984170_SNP [dm6]	G	A	3.551e^-5	1	INTRON Grip
2L	7357472	2L_7357472_SNP [dm3] 2L_7357472_SNP [dm6]	G	T	3.917e^-5	1	INTERGENIC
2R	8667970	2R_8667970_SNP [dm3] 2R_12780465_SNP [dm6]	T	G	3.967e^-5	1	UPSTREAM sca INTERGENIC	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_ftz BDTNP1_TFBS_hb BDTNP1_TFBS_kni BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
X	17210042	X_17210042_SNP [dm3] X_17316009_SNP [dm6]	A	T	4.050e^-5	1	INTRON B-H2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl mE1_TFBS_cad
2R	12700674	2R_12700674_SNP [dm3] 2R_16813169_SNP [dm6]	A	G	4.180e^-5	1	DOWNSTREAM CR44379 INTERGENIC
3L	2658044	3L_2658044_SNP [dm3] 3L_2658044_SNP [dm6]	T	C	4.675e^-5	1	INTRON Fife	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_ftz BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_chinmo mE1_TFBS_HSA
2L	7357473	2L_7357473_INS [dm3] 2L_7357473_INS [dm6]	A	ATATAATAG	4.687e^-5	1	INTERGENIC
X	6076395	X_6076395_SNP [dm3] X_6182362_SNP [dm6]	T	C	4.821e^-5	1	INTRON Ca-alpha1T
3L	5357382	3L_5357382_SNP [dm3] 3L_5364282_SNP [dm6]	G	C	4.898e^-5	1	INTRON Uev1A
3L	12523440	3L_12523440_DEL [dm3] 3L_12530340_DEL [dm6]	TTAGCGCACATATT...	T	4.919e^-5	1	UPSTREAM nst DOWNSTREAM Tsf2 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_D mE1_TFBS_HSA
2L	15814137	2L_15814137_SNP [dm3] 2L_15814137_SNP [dm6]	G	A	5.293e^-5	1	INTERGENIC
2L	3010720	2L_3010720_SNP [dm3] 2L_3010720_SNP [dm6]	G	C	5.340e^-5	1	INTRON CG17265
2L	3927061	2L_3927061_SNP [dm3] 2L_3927061_SNP [dm6]	C	T	5.436e^-5	1	INTRON fred	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2R	19896168	2R_19896168_INS [dm3] 2R_24008645_INS [dm6]	A	ACATA	5.454e^-5	1	INTRON Unc-89	TF binding site mE1_TFBS_cad
2L	20488899	2L_20488899_SNP [dm3] 2L_20488899_SNP [dm6]	C	T	6.131e^-5	1	UPSTREAM CR45359 DOWNSTREAM CR45360 INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
3L	18397873	3L_18397873_SNP [dm3] 3L_18404773_SNP [dm6]	T	A	6.304e^-5	1	INTERGENIC	regulatory region REDfly_CRMs TF binding site mE1_TFBS_sbb
3L	14674119	3L_14674119_SNP [dm3] 3L_14681019_SNP [dm6]	G	C	6.363e^-5	1	INTRON ome
2L	11741452	2L_11741452_SNP [dm3] 2L_11741452_SNP [dm6]	C	T	6.468e^-5	1	INTRON Vha100-5	TF binding site mE1_TFBS_chinmo
2L	12762889	2L_12762889_SNP [dm3] 2L_12762889_SNP [dm6]	T	C	6.568e^-5	1	INTERGENIC
3L	14675888	3L_14675888_SNP [dm3] 3L_14682788_SNP [dm6]	G	C	6.940e^-5	1	INTRON ome
3L	14672390	3L_14672390_SNP [dm3] 3L_14679290_SNP [dm6]	A	C	6.962e^-5	1	INTRON ome
2L	2123214	2L_2123214_SNP [dm3] 2L_2123214_SNP [dm6]	G	A	7.018e^-5	1	INTERGENIC
X	16278780	X_16278780_SNP [dm3] X_16384747_SNP [dm6]	C	A	7.202e^-5	1	UTR_5_PRIME CG9992 UPSTREAM CG9992 & 1 other	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_Trl mE1_TFBS_Ubx
3L	5440452	3L_5440452_SNP [dm3] 3L_5447352_SNP [dm6]	C	T	7.414e^-5	1	INTERGENIC
3L	5357381	3L_5357381_SNP [dm3] 3L_5364281_SNP [dm6]	G	A	7.420e^-5	1	INTRON Uev1A
3L	3918817	3L_3918817_SNP [dm3] 3L_3918817_SNP [dm6]	C	T	7.581e^-5	1	INTRON Eip63F-1
2L	7357517	2L_7357517_SNP [dm3] 2L_7357517_SNP [dm6]	T	C	7.707e^-5	1	INTERGENIC
2R	15272798	2R_15272798_SNP [dm3] 2R_19385293_SNP [dm6]	A	G	7.950e^-5	1	UPSTREAM CG10081 DOWNSTREAM CG10073 INTERGENIC
3R	20460830	3R_20460830_SNP [dm3] 3R_24635108_SNP [dm6]	C	T	7.951e^-5	1	UTR_5_PRIME CG43222 UPSTREAM CG43222 DOWNSTREAM puf & 1 other
3R	25160685	3R_25160685_SNP [dm3] 3R_29334963_SNP [dm6]	C	G	7.978e^-5	1	INTERGENIC
X	12517230	X_12517230_SNP [dm3] X_12623197_SNP [dm6]	G	A	8.056e^-5	1	DOWNSTREAM CR44568 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	5440408	3L_5440408_SNP [dm3] 3L_5447308_SNP [dm6]	A	T	8.295e^-5	1	INTERGENIC
3L	8525089	3L_8525089_SNP [dm3] 3L_8531989_SNP [dm6]	A	G	8.995e^-5	1	SYNONYMOUS_CODING foi	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
X	16279021	X_16279021_SNP [dm3] X_16384988_SNP [dm6]	A	C	9.053e^-5	1	UPSTREAM CG9992 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_h mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_jumu mE1_TFBS_Trl mE1_TFBS_Ubx
2L	3926659	2L_3926659_SNP [dm3] 2L_3926659_SNP [dm6]	C	T	9.116e^-5	1	INTRON fred	TF binding site mE1_TFBS_bab1
3R	17067033	3R_17067033_SNP [dm3] 3R_21241311_SNP [dm6]	T	A	9.151e^-5	1	INTERGENIC	regulatory region REDfly_CRMs
3L	11880583	3L_11880583_SNP [dm3] 3L_11887483_SNP [dm6]	T	C	9.193e^-5	1	UTR_3_PRIME CG5897 INTRON CG44837
2L	13965633	2L_13965633_SNP [dm3] 2L_13965633_SNP [dm6]	G	A	9.307e^-5	1	SYNONYMOUS_CODING NimB2 DOWNSTREAM NimB1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	11906555	3L_11906555_SNP [dm3] 3L_11913455_SNP [dm6]	T	G	9.720e^-5	1	INTRON CG44837
X	12517267	X_12517267_SNP [dm3] X_12623234_SNP [dm6]	C	A	1.009e^-4	1	DOWNSTREAM CR44568 INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
2L	7357423	2L_7357423_SNP [dm3] 2L_7357423_SNP [dm6]	T	C	1.027e^-4	1	INTERGENIC
2L	12762833	2L_12762833_SNP [dm3] 2L_12762833_SNP [dm6]	C	T	1.085e^-4	1	UPSTREAM CG15483 INTERGENIC
2R	9932897	2R_9932897_SNP [dm3] 2R_14045392_SNP [dm6]	A	G	1.090e^-4	1	INTRON mam	TF binding site mE1_TFBS_sens
3L	1603436	3L_1603436_SNP [dm3] 3L_1603436_SNP [dm6]	C	T	1.092e^-4	1	UPSTREAM CG12104 INTRON CG33791 & 1 other	TF binding site mE1_TFBS_cad
3L	13241658	3L_13241658_SNP [dm3] 3L_13248558_SNP [dm6]	T	C	1.100e^-4	1	SYNONYMOUS_CODING CG32119 UPSTREAM tRNA:D2:69F INTRON caps
2L	8351480	2L_8351480_SNP [dm3] 2L_8351480_SNP [dm6]	T	C	1.114e^-4	1	UPSTREAM Mur29B DOWNSTREAM CG7778 INTERGENIC
2L	17538172	2L_17538172_SNP [dm3] 2L_17538172_SNP [dm6]	A	T	1.130e^-4	1	INTERGENIC
3L	4026193	3L_4026193_SNP [dm3] 3L_4026193_SNP [dm6]	T	C	1.133e^-4	1	UPSTREAM CG11594 & 1 other INTERGENIC
2L	3926865	2L_3926865_SNP [dm3] 2L_3926865_SNP [dm6]	T	G	1.218e^-4	1	INTRON fred	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad
2L	13965681	2L_13965681_SNP [dm3] 2L_13965681_SNP [dm6]	C	T	1.241e^-4	1	SYNONYMOUS_CODING NimB2 DOWNSTREAM NimB1	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22447994	3R_22447994_SNP [dm3] 3R_26622272_SNP [dm6]	G	T	1.245e^-4	1	UPSTREAM TwdlP DOWNSTREAM TwdlB INTERGENIC
3L	321932	3L_321932_SNP [dm3] 3L_321932_SNP [dm6]	C	T	1.254e^-4	1	SYNONYMOUS_CODING CG32344	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_HSA mE1_TFBS_sens
2L	3927263	2L_3927263_SNP [dm3] 2L_3927263_SNP [dm6]	C	T	1.258e^-4	1	INTRON fred	TF binding site mE1_TFBS_bab1 mE1_TFBS_cad mE1_TFBS_HSA
X	16421033	X_16421033_SNP [dm3] X_16527000_SNP [dm6]	C	G	1.269e^-4	1	INTRON para	TF binding site BDTNP1_TFBS_dl
2L	7341261	2L_7341261_INS [dm3] 2L_7341261_INS [dm6]	T	TT	1.272e^-4	1	INTRON Wnt6	TF binding site mE1_TFBS_sbb
2L	12762954	2L_12762954_SNP [dm3] 2L_12762954_SNP [dm6]	A	T	1.275e^-4	1	INTERGENIC
X	16421048	X_16421048_SNP [dm3] X_16527015_SNP [dm6]	T	G	1.303e^-4	1	INTRON para	TF binding site BDTNP1_TFBS_dl
2L	16334415	2L_16334415_SNP [dm3] 2L_16334415_SNP [dm6]	C	G	1.325e^-4	1	SYNONYMOUS_CODING CG31817	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	3588594	3L_3588594_SNP [dm3] 3L_3588594_SNP [dm6]	A	C	1.346e^-4	1	INTRON Eip63E
2R	7816470	2R_7816470_SNP [dm3] 2R_11928965_SNP [dm6]	C	T	1.347e^-4	1	DOWNSTREAM CR44312 INTERGENIC
3L	12696493	3L_12696493_SNP [dm3] 3L_12703393_SNP [dm6]	A	C	1.348e^-4	1	INTRON mirr	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_slp1 BDTNP1_TFBS_twi mE1_TFBS_HSA
X	5449728	X_5449728_SNP [dm3] X_5555695_SNP [dm6]	C	A	1.367e^-4	1	INTRON Vsx2	TF binding site mE1_TFBS_cnc mE1_TFBS_Kr
2L	1094421	2L_1094421_SNP [dm3] 2L_1094421_SNP [dm6]	T	C	1.390e^-4	1	INTRON CG4629
2L	10774986	2L_10774986_SNP [dm3] 2L_10774986_SNP [dm6]	C	A	1.391e^-4	1	INTRON CG31869
3R	25160577	3R_25160577_SNP [dm3] 3R_29334855_SNP [dm6]	C	A	1.394e^-4	1	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb
X	6776890	X_6776890_SNP [dm3] X_6882857_SNP [dm6]	C	T	1.421e^-4	1	INTERGENIC
2R	13062820	2R_13062820_SNP [dm3] 2R_17175315_SNP [dm6]	A	T	1.422e^-4	1	INTERGENIC
2R	8548989	2R_8548989_SNP [dm3] 2R_12661484_SNP [dm6]	T	A	1.423e^-4	1	UTR_5_PRIME nemy INTRON nemy
X	5557494	X_5557494_SNP [dm3] X_5663461_SNP [dm6]	C	T	1.486e^-4	1	UPSTREAM CG42265 EXON CR45520	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
2L	15202113	2L_15202113_SNP [dm3] 2L_15202113_SNP [dm6]	C	A	1.501e^-4	1	UPSTREAM CR43357 & 1 other INTERGENIC
2L	13426671	2L_13426671_SNP [dm3] 2L_13426671_SNP [dm6]	T	G	1.535e^-4	1	INTRON CG42784
2R	18631020	2R_18631020_SNP [dm3] 2R_22743515_SNP [dm6]	T	G	1.553e^-4	1	UTR_3_PRIME CG42260	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
X	16277764	X_16277764_SNP [dm3] X_16383731_SNP [dm6]	A	T	1.555e^-4	1	UPSTREAM CG9992 INTRON CG9992	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi
2L	4825286	2L_4825286_SNP [dm3] 2L_4825286_SNP [dm6]	G	A	1.609e^-4	1	INTRON CG15628
2L	4825342	2L_4825342_SNP [dm3] 2L_4825342_SNP [dm6]	A	C	1.609e^-4	1	INTRON CG15628
3L	2616188	3L_2616188_SNP [dm3] 3L_2616188_SNP [dm6]	C	T	1.648e^-4	1	INTRON Pxn	TF binding site mE1_TFBS_chinmo
3R	21680788	3R_21680788_SNP [dm3] 3R_25855066_SNP [dm6]	A	G	1.655e^-4	1	INTERGENIC
X	6629712	X_6629712_SNP [dm3] X_6735679_SNP [dm6]	A	G	1.676e^-4	1	INTRON CG3168 EXON CR43461
2R	19896143	2R_19896143_SNP [dm3] 2R_24008620_SNP [dm6]	C	A	1.681e^-4	1	INTRON Unc-89	TF binding site mE1_TFBS_cad
2R	19896162	2R_19896162_INS [dm3] 2R_24008639_INS [dm6]	A	ATA	1.683e^-4	1	INTRON Unc-89	TF binding site mE1_TFBS_cad
2L	18295252	2L_18295252_SNP [dm3] 2L_18295252_SNP [dm6]	A	G	1.687e^-4	1	NON_SYNONYMOUS_CODING CG5790	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
X	5050351	X_5050351_SNP [dm3] X_5156318_SNP [dm6]	G	A	1.717e^-4	1	INTRON rg & 1 other
X	12529937	X_12529937_SNP [dm3] X_12635904_SNP [dm6]	G	A	1.719e^-4	1	UTR_5_PRIME Tomosyn UPSTREAM mir-970
2L	3109308	2L_3109308_SNP [dm3] 2L_3109308_SNP [dm6]	A	T	1.731e^-4	1	UPSTREAM PpD6 INTRON toc	TF binding site mE1_TFBS_inv
2L	4027148	2L_4027148_SNP [dm3] 2L_4027148_SNP [dm6]	A	G	1.731e^-4	1	INTERGENIC
2R	16228682	2R_16228682_INS [dm3] 2R_20341177_INS [dm6]	T	TCTT	1.745e^-4	1	UPSTREAM CG16739 INTERGENIC
2R	8549149	2R_8549149_INS [dm3] 2R_12661644_INS [dm6]	T	TCT	1.764e^-4	1	UTR_5_PRIME nemy INTRON nemy
3L	7779154	3L_7779154_SNP [dm3] 3L_7786054_SNP [dm6]	A	T	1.773e^-4	1	INTRON CG32369
3L	2962429	3L_2962429_SNP [dm3] 3L_2962429_SNP [dm6]	A	G	1.787e^-4	1	NON_SYNONYMOUS_CODING Or63a
2R	17563428	2R_17563428_SNP [dm3] 2R_21675923_SNP [dm6]	A	G	1.801e^-4	1	INTRON CG30263	TF binding site mE1_TFBS_HSA mE1_TFBS_sbb

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By genomic position
Variant impact
Gene name

mn_Glucose phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results